1R1X

Crystal structure of oxy-human hemoglobin Bassett at 2.15 angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

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This is version 1.4 of the entry. See complete history


Literature

Characterization of hemoglobin bassett (alpha94Asp-->Ala), a variant with very low oxygen affinity

Abdulmalik, O.Safo, M.K.Lerner, N.B.Ochotorena, J.Daikhin, Y.Lakka, V.Santacroce, R.Abraham, D.J.Asakura, T.

(2004) Am J Hematol 77: 268-276

  • DOI: 10.1002/ajh.20184
  • Primary Citation of Related Structures:  
    1R1X, 1R1Y

  • PubMed Abstract: 
  • Hemoglobin (Hb) Bassett, an abnormal Hb variant with a markedly reduced oxygen affinity, was discovered in a Caucasian (Anglo-Saxon) male child who experienced episodes of cyanosis. Cation-exchange and reversed-phase (RP) high-performance liquid chromatography (HPLC) showed that the patient has an abnormal Hb, with a mutation in the alpha-globin ...

    Hemoglobin (Hb) Bassett, an abnormal Hb variant with a markedly reduced oxygen affinity, was discovered in a Caucasian (Anglo-Saxon) male child who experienced episodes of cyanosis. Cation-exchange and reversed-phase (RP) high-performance liquid chromatography (HPLC) showed that the patient has an abnormal Hb, with a mutation in the alpha-globin. Tryptic peptide digest of the abnormal alpha-globin with subsequent HPLC analysis revealed abnormal elution of the alpha-T11 peptide. Further studies with Edman sequencing and electrospray mass spectrometry of tryptic peptide alpha-T11, as well as structural analysis by X-ray crystallography revealed an Asp-->Ala substitution at the alpha94 (G1) position, a match for Hb Bassett. Detailed functional studies showed that this Hb variant had a markedly reduced oxygen affinity (P(50) at pH 7.0 = 22 mmHg; Hb A P(50) = 10.5 mmHg), reduced Bohr effect (-0.26 compared to - 0.54 in Hb A), and low subunit cooperativity (n = 1.4, compared to 2.6 in Hb A). X-ray crystallography results explain the probable effects of the structural modification on the oxygen-binding properties of this Hb variant.


    Organizational Affiliation

    Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin alpha chainA141Homo sapiensMutation(s): 1 
Gene Names: HBA1HBA2
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens)
Explore P69905 
Go to UniProtKB:  P69905
PHAROS:  P69905
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69905
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin beta chainB146Homo sapiensMutation(s): 0 
Gene Names: HBB
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens)
Explore P68871 
Go to UniProtKB:  P68871
PHAROS:  P68871
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68871
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
MBN
Query on MBN

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
TOLUENE
C7 H8
YXFVVABEGXRONW-UHFFFAOYSA-N
 Ligand Interaction
CMO
Query on CMO

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.357α = 90
b = 53.357β = 90
c = 191.781γ = 90
Software Package:
Software NamePurpose
CNSrefinement
bioteXdata reduction
bioteXdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-07
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2018-08-29
    Changes: Data collection, Database references